See the on-line Independent Modeling Projects:

• Katianna Pihakari: Molecular Dynamics Simulation STudy of the Hinge-Bending Motion of the Bacteriophage M61 T4 Lysozyme
• Sonia Gupta: Modeling of Dynamics of Protein G
• Rolf Minkwitz: FGF Binding and FGF Receptor Activation by Synthetic Heparan-Derived Di- and Trisaccharides
• Vikas Bhandawat: Modeling of Delta and Notch Proteins of Drosophila
• Rose Liang: QSAR Studies of Glycogen Phosphorelase Inhibitors
• Michael Pacold: Testing Molecular Simulations with Minichaperones

Table of Contents

• Goals of the Course
• Course Syllabus
• Course Format
• Individual Modeling Projects
• Course Materials
• Course Grades

This course is designed for the graduate-level student with a basic knowledge of biomolecular structure. A basic familiarity with UNIX computing is recommended, but not required. If you have little or no experience with UNIX computing, contact Marty.

You must also complete an On-Line UNIX Exam by Friday, Jan. 22. If you fail to take the exam at least once on or before Jan. 22, you will fail the course. This exam may be taken at any time on or before this date, and may be taken more than once (only your last attempt to take this exam will be graded). The purpose of this exam is to give you confidence that you are sufficiently familiar with UNIX. Your exam score will NOT be incorporated into your final course grade. However, if your exam score is insufficient, you may be asked to repeat the exam until your score is sufficient. In these cases, there will be no deadline for repeating the exam, but I will expect you to repeat the exam in a timely manner.

There will also be a mid-term exam on March 10. This exam will consist of multiple choice, "fill-in-the-blank", and "short answer" questions covering the course material. ALL potential exam questions & answers will be posted on this web site by 1:30pm, Thursday, March 4, and will also be available in hardcopy form at my Office Hour on March 4. The list will include approximately 300 questions & answers, but only a subset of these questions will appear on the exam. No books, notes, or other educational material will be allowed to be available during the exam. The purpose of this exam is to give you confidence that you have developed a adequate understanding of computing methods in biochemistry.

During the second half of the course, you will accomplish an Individual Modeling Project that applies one or more computing methods to a specific biochemical problem. Details about the Individual Modeling Project assignment are listed below. During this portion of the course, there will be no scheduled class meetings. Instead, you will work independently according to your own schedule. I strongly encourage you to invest time and effort throughout the second half of the course, instead of waiting until the end of this period to accomplish your work. I will be monitoring your usage of the computer workstations (through standard UNIX accounting procedures), and I will contact you if your computing usage is noticably absent for long periods in March and early April.

There will also be no scheduled Office Hours while you are accomplishing your Individual Modeling Project. Instead, you can arrange to meet with me or John Taraszka at a mutually convenient time. I strongly encourage you to meet with John or me "too often" rather than "not often enough". I will also likely meet with you on an informal, impromptu basis while you are working on your Individual Modeling Project in A701. Also, your C687 colleagues can often provide very helpful advice during this portion of the course.

A Modeling Project Proposal will be due at 5pm on Friday, March 5. If you fail to submit a proposal by March 5, you will fail the course. Evaluation of your proposal will NOT be included in your course grade. I may meet with you to discuss your proposal shortly after March 5, during which I may ask you to submit a revised proposal. The purpose of this proposal is to help ensure that your Individual Modeling Project is feasible and sufficiently covers the goals of the course. I also encourage you to discuss your proposal with me at any time BEFORE March 5.

A Modeling Paper describing your Individual Modeling Project will be due at 5pm on April 30. Details about the Modeling Paper assignment are listed below.

During the Wednesday of Finals Week (May 5), there will be a 3-hour poster session where you will present the results of your modeling project in poster form to other class members and invited faculty, post-docs, graduate students, undergraduates, and staff members from the Departments of Chemistry and Biology. You will be expected to be present near your poster during a portion of this 3-hour period, so that you can discuss your work with C687 colleagues, other visitors, and me.

Final course grades will be available on Friday, May 7.

1. Choose and design your own project. Choose a topic that is of biochemical interest to you (e.g. it might involve compounds being studied in your reserach laboratory), and a project in which you will learn computing methods that will be of interest to you in the future. Choose a project that can be realistically achieved in the available time (e.g. choose relatively small molecules, or a subset of a larger molecule, if possible). If you have questions about the choice, scope, feasibility, etc. of your Modeling Project Proposal, contact me as soon as possible. If you have difficulty designing a suitable project, I have several project ideas that have been provided by IU research labs.

2. Modeling Project Proposal: Write a 2-3 page proposal summarizing your proposed project and submit this no later than 5pm, Friday, March 5. This should be formatted like a mini-grant proposal. Include the following sections:
   1. ABSTRACT: a project summary specifying the goals of the project
   2. INTRODUCTION/BACKGROUND: a BRIEF summary of the relevant scientific background and reasons why the current project is of interest.
   3. METHODS & PROCEDURES: the computing methods & procedures you intend to use to study the biochemical problem
   4. INTENDED CONCLUSIONS: how you intend to evaluate the strengths and weaknesses of the computing method, and how you intend to interpret & apply the modeling results to the biochemical problem
   5. how you plan to disseminate your results---let me know if you will submit your Modeling Paper in hardcopy form, as an html page, a Microsoft Word file, etc.
   6. Which section of the Poster Session would be appropriate for your poster:
      1. Sequence Alignment & Sequence Homology Modeling
      2. Energy Minimization & Dynamics
      3. Modeling of Molecular Properties
      4. Docking & Ligand Design
      5. or suggest a new category

   See also the
   EXAMPLE OF AN INDEPENDENT MODELING PROJECT PROPOSAL

   Good Individual Modeling Projects are usually founded by a good Proposal. Use the Proposal as an opportunity to learn more about the techniques you will use and to formulate efficient strategies to answer your scientific questions. Also use the Proposal to choose and develop a realistic modeling experiment that can be accomplished in a relatively short period of time. Past experiences have shown that a well-designed Proposal will save you lots of time and effort when you actually work on the project.

3. Do the project. This will be done mostly in your own time between March 22 and April 30. Typically, you should expect to spend about 5-7 hours per week on your project during this period. I strongly encourage you to invest time and effort throughout the second half of the course, instead of waiting until the end of this period to accomplish your work. I will be monitoring your usage of the computer workstations (through standard UNIX accounting procedures), and I will contact you if your computing usage is noticably absent for long periods in March and early April.

4. Modeling Paper: Write a Modeling Paper summarizing the results of your project. This paper should be at least 3 pages; while there is no maximum length, all relevant material should be included in the shortest number of pages. The format of the paper depends on the project you chose, but should be similar to the format of a journal manuscript. The content of the paper should include:
   1. ABSTRACT: a project summary specifying the goals of the project
   2. INTRODUCTION/BACKGROUND: a summary of the relevant biochemical background and reasons why the current project is of interest
   3. METHODS & PROCEDURES: the computing methods & procedures you used to study the biochemical problem
   4. RESULTS
   5. CONCLUSIONS: your evaluation of the strengths and weaknesses of the computing method(s), and your interpretation & application of the modeling results to the biochemical problem. Also include a brief section about your plans for the future (e.g., how would you repeat the modeling, continue the modeling, or extend the modeling if you continued to work on the project after this semester).
   6. REFERENCES
   7. LIST OF FIGURES: Figures do NOT have to be incorporated into the text. Instead, they can be included at the end (a common format for manuscripts). All figures should have a caption; the caption can appear on the same page as the figure, or a separate "figure caption page" can list all figure captions (again, a common format for manuscripts). Figures may be in color or black & white.
   8. APPENDIX: an optional section listing relevant modeling data. It may also include a brief tutorial for the rest of the class explaining how to use a particular modeling technique. The appendix should NOT be used just to add extra pages to your paper.

   I encourage you to submit your paper in electronic format (e.g., html, Word document on disk) instead of hardcopy, but hardcopy is entirely acceptable. The Modeling Paper is due at 5pm on Friday, April 30.

5. Modeling Poster: Prepare a Modeling Poster summarizing the results of your project. The format of the poster depends on the project you chose. Emphasis should be placed on VISUALIZATION: your poster must summarize your Individual Modeling Project to people who will spend no more than ~2 minutes reading your poster. Therefore, even though the content of your Modeling Poster and Modeling Paper will probably be extremely similar, your poster should be more of a summary of the paper's contents.

   You may continue to develop your poster until the start of the Poster Session, at 1:30 on Wednesday, May 5. Your poster will be displayed from 1:30-4:30 on May 5, next to other posters in the same category. You will be required to be near your poster for a portion of this display time. Other class members and invited faculty, post-docs, graduate students, undergraduates, and staff members from the Departments of Chemistry and Biology will be present at the poster session. After the Poster session, you can reposess your poster or donate your poster to the Molecular Visualization Facility (so that it can be displayed in A701 and used as an example for future C687 courses).

   Poster presentation space will be limited to 4 feet by 4 feet. Poster material can be posted to the supplied styrofoam bulletin boards with tape or push pins.

• Molecular Modeling: Basic Principles and Applications
  Authors: Holtje & Folkers
  Year: 1997
  Location in Chemistry Library: QP517.M3 H64
  An excellent, very readable text describing classical force fields, minimization, and dynamics, electrostatic potentials and other molecular properties, sequence alignments, docking, and ligand design. This text has two very good case studies---one for small molecules and one for large molecules.
• Theory and Methodology Section of the On-line Discover Manuals (ONLY Accessible from SGI workstations in the Department of Chemistry that are connected to the MolViz Server). This information is also available in hardcopy form in the Discover Part 1 version 95.0 Manual available in A701. Manuals in A701 must not leave this room without permission from the MolViz Facility Staff (Ken DeHart, John Taraszka, or me).

There are a variety of recommended sources of information on this web site, including:

• The MolViz Application Guide
• On-line Discover Manuals (ONLY Accessible from SGI workstations in the Department of Chemistry that are connected to the MolViz Server)
• Scream Saver Newsletters from the MolViz Facility
• Links to other Molecular Modeling WWW sites
• Links to other UNIX WWW sites

See the Molecular Modeling Publications and UNIX Publications for other sources of information. If you check out one of these textbooks from the Chemistry Library, please return the text in a timely manner so that others can benefit from the text. If you want to read a textbook that is on this list, but is not available in the library, contact me.